Hi Jonathan, this may also be a result of too strong SS bond restraints or/and inaccurate SS bond restraints parameters or/and disorder (in some fraction of unit cells there is no SS bond). More on the topic:
"Disulfide bond restraints" here: http://phenix-online.org/newsletter/CCN_2015_01.pdf#page=13 Pavel On Mon, May 27, 2019 at 6:20 AM Jonathan Cooper < 00000c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote: > When you refine structures with disulphide bridges you often get negative > difference density for the sulphurs, presumably due to the well-known > radiation damage effects. The negative difference density often won't > disappear with usual B-factor refinement. However, it seems to go away if > you refine the occupancy of the affected sulphur atoms e.g. to 0.9 or > thereabouts. Would it be acceptable to publish/deposit structures where the > sulphur occupancy is less than one, given a suitable REMARK in the pdb > file? Thank you. > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
